Part 6: Working With OWL

OAK exposes an experimental funowl adapter for local OWL files. The selector name is historical; the adapter is now backed by py-horned-owl. Plain local .owl, .ofn, .omn, and .owx paths default to this adapter; explicit schemes such as sqlite:foo.owl still override that default.

OWL Datamodel

See funowl

OwlInterface

OwlInterface is the low-level OAK view for working with OWL axioms and OWL- specific structures directly.

Loading a local OWL file

For local files, plain .owl, .ofn, .omn, and .owx paths now default to the horned-owl-backed OWL adapter:

from oaklib import get_adapter

oi = get_adapter("path/to/my-ontology.owl")
print(type(oi).__name__)

If you want a different backend, be explicit in the selector:

sqlite_oi = get_adapter("sqlite:path/to/my-ontology.owl")
sparql_oi = get_adapter("sparql:path/to/my-ontology.owl")

Inspecting asserted OWL axioms

You can iterate over raw axioms, or use helpers for common axiom types:

from oaklib import get_adapter

oi = get_adapter("path/to/my-ontology.owl")

for axiom in oi.subclass_axioms(subclass="GO:0005634"):
    print(type(axiom).__name__, axiom)

labels = list(
    oi.annotation_assertion_axioms(
        subject="GO:0005634",
        property="rdfs:label",
    )
)

eq_axioms = list(oi.equivalence_axioms(about="GO:0031965"))

If you need the underlying horned-owl ontology object, use:

ontology = oi.owl_ontology()
print(type(ontology).__name__)

Projected graph operations

The horned-owl adapter also projects a graph view from supported OWL patterns, so graph-oriented APIs can often be used alongside axiom APIs:

from oaklib import get_adapter

oi = get_adapter("path/to/my-ontology.owl")

direct = list(oi.relationships(subjects=["GO:0005634"]))
entailed = list(
    oi.relationships(
        subjects=["GO:0005634"],
        include_entailed=True,
    )
)
ancestors = list(oi.ancestors("GO:0005634", predicates=["rdfs:subClassOf"]))

Logical definitions are exposed in OBO Graph form:

ldefs = list(oi.logical_definitions(subjects=["GO:0031965"]))
for ldef in ldefs:
    print(ldef.definedClassId, ldef.genusIds, ldef.restrictions)

Reasoning status

OwlInterface does not currently provide a pluggable OWL reasoner. In the current horned-owl-backed implementation:

• reasoner_configurations() returns an empty list

• axiom filtering does not accept a ReasonerConfiguration

• include_entailed=True on graph methods gives a lightweight projected closure over supported OWL patterns, not full OWL reasoning

For precomputed closure and broader graph-style querying, the recommended production path remains the SQL Database Adapter. For external OWL reasoners, see the ROBOT plugin below.

ROBOT Plugin

See oakx-robot